SEMINAR REPORT On PROTEIN BASED OPTICAL MEMORY Submitted by ANUJ KUMAR in partial fulfillment for the award of the degree of BACHELOR OF TECHNOLOGY in COMPUTER SCIENCE & ENGINEERING SCHOOL OF ENGINEERING COCHIN UNIVERSITY OF SCIENCE AND TECHNOLOGY, KOCHI – 682022 SEPTEMBER 2008
29
Embed
SEMINAR REPORT On - 123seminarsonly.com · SEMINAR REPORT On PROTEIN BASED ... ANUJ KUMAR in partial fulfillment for the award of the degree of BACHELOR OF TECHNOLOGY in ... • …
This document is posted to help you gain knowledge. Please leave a comment to let me know what you think about it! Share it to your friends and learn new things together.
Transcript
SEMINAR REPORT
On
PROTEIN BASED OPTICAL MEMORYSubmitted by
ANUJ KUMAR
in partial fulfillment for the award of the degree
of
BACHELOR OF TECHNOLOGY
in
COMPUTER SCIENCE & ENGINEERING
SCHOOL OF ENGINEERING
COCHIN UNIVERSITY OF SCIENCE AND TECHNOLOGY,
KOCHI – 682022
SEPTEMBER 2008
DIVISION OF COMPUTER SCIENCE & ENGINEERING
SCHOOL OF ENGINEERING
COCHIN UNIVERSITY OF SCIENCE & TECHNOLOGY,
KOCHI – 682022
Certificate
This is to certify that the seminar report entitled “PROTEIN BASED
OPTICAL MEMORY” submitted by ANUJ KUMAR, semester VII, in
partial fulfillment of the requirement of the award of B-Tech degree in
COMPUTER SCIENCE AND ENGINEERING, Cochin University of
Science and Technology, is a bonafide record of the seminar presented by him
during the academic year 2008.
.
Ms. Ancy Zachariah Seminar Guide
Mr. David Peter S Head of the Department
Place: KochiDate:
Acknowledgement
At the outset, we thank God almighty for making our endeavor a success. We also express
our gratitude to Dr. David Peter, Head of the Department, Division of Computer
Engineering for providing us with adequate facilities, ways and means by which we were
able to complete this seminar.
We express our sincere gratitude to our Seminar Guide Ms. Ancy Zachariah, Lecturer,
Division of Computer Engineering for her constant support and valuable suggestions without
which the successful completion of this seminar would not have been possible.
We express our immense pleasure and thankfulness to all the teachers and staff of the
Department of Computer Engineering, CUSAT for their cooperation and support.
Last but not the least, we thank all others, and especially our classmates and our family
members who in one way or another helped us in the successful completion of this work.
ANUJ KUMAR
Table Of Contents
CHAPTER No. TITLE PAGE NO.
Abstract vi List Of Figures v
1 Introduction 1
2 Memory Research and Development 4
2.1 Semiconductor Memory Developments 6
2.2 3 – D Optical Memories 6
3 Protein – Based Memory 8
3.1 Development 8
3.2 Process of Protein Extraction 12
3.3 BacterioRhodopsin Photocycle 13
3.4 Data operation 16
3.4.1 Data – Writing Technique 16
3.4.2 Data – Reading Technique 18
3.4.3 Data Erasing 19
3.4.4 Refreshing the Memory 19
4 Intrinsic Worth 21
5 Conclusion 22
6 References 23
iv
List of Figures
Figure No. Title Page No.
3.3.1 This is the chromophore 17
3.3.2 The photocycle for computer memory 20
3.4.1 The write process 22
3.4.2 The read process 23
3.5 Actual Implementation 25
v
Abstract
While magnetic and semi-conductor based information storage devices have been in use
since the middle 1950's, today's computers and volumes of information require
increasingly more efficient and faster methods of storing data. While the speed of
integrated circuit random access memory (RAM) has increased steadily over the past ten
to fifteen years, the limits of these systems are rapidly approaching. In response to the
rapidly changing face of computing and demand for
• physically smaller,
• greater capacity,
• bandwidth,
A number of alternative methods to integrated circuit information storage have surfaced
recently. Among the most promising of the new alternatives are
• photopolymer-based devices,
• holographic optical memory storage devices, and
• protein-based optical memory storage using rhodopsin ,
• Photosynthetic reaction centers, cytochrome c, photosystems I and II,
phycobiliproteins, and phytochrome.
This article focuses mainly on protein-based optical memory storage using the
photosensitive protein bacteriorhodopsin with the two-photon method of exciting the
molecules, but briefly describes what is involved in the other two. Bacteriorhodopsin is a
light-harvesting protein from bacteria that live in salt marshes that has shown some
promise as feasible optical data storage. The current work is to hybridize this biological
molecule with the solid state components of a typical computer.
vi
Protein Based Optical Memory
1. Introduction
Since the dawn of time, man has tried to record important events and techniques for
everyday life. At first, it was sufficient to paint on the family cave wall how one
hunted. Then came the people who invented spoken languages and the need arose to
record what one was saying without hearing it firsthand. Therefore, years later, earlier
scholars invented writing to convey what was being said. Pictures gave way to letters
which represented spoken sounds. Eventually clay tablets gave way to parchment,
which gave way to paper. Paper was, and still is, the main way people convey
information. However, in the mid twentieth century computers began to come into
general use . . .
Computers have gone through their own evolution in storage media. In the
forties, fifties, and sixties, everyone who took a computer course used punched cards
to give the computer information and store data. In 1956, researchers at IBM
developed the first disk storage system. This was called RAMAC (Random Access
Method of Accounting and Control)
Since the days of punch cards, computer manufacturers have strived to
squeeze more data into smaller spaces. That mission has produced both competing
and complementary data storage technology including electronic circuits, magnetic
media like hard disks and tape, and optical media such as compact disks.
Today, companies constantly push the limits of these technologies to improve
their speed, reliability, and throughput -- all while reducing cost. The fastest and most
expensive storage technology today is based on electronic storage in a circuit such as
a solid state "disk drive" or flash RAM. This technology is getting faster and is able to
store more information thanks to improved circuit manufacturing techniques that
shrink the sizes of the chip features. Plans are underway for putting up to a gigabyte
of data onto a single chip.
Department of Computer Engineering
1
Protein Based Optical Memory
Magnetic storage technologies used for most computer hard disks are the most
common and provide the best value for fast access to a large storage space. At the low
end, disk drives cost as little as 25 cents per megabyte and provide access time to data
in ten milliseconds. Drives can be ganged to improve reliability or throughput in a
Redundant Array of Inexpensive Disks (RAID). Magnetic tape is somewhat slower
than disk, but it is significantly cheaper per megabyte. At the high end, manufacturers
are starting to ship tapes that hold 40 gigabytes of data. These can be arrayed together
into a Redundant Array of Inexpensive Tapes (RAIT), if the throughput needs to be
increased beyond the capability of one drive.
For randomly accessible removable storage, manufacturers are beginning to
ship low-cost cartridges that combine the speed and random access of a hard drive
with the low cost of tape. These drives can store from 100 megabytes to more than
one gigabyte per cartridge.
Standard compact disks are also gaining a reputation as an incredibly cheap
way of delivering data to desktops. They are the cheapest distribution medium around
when purchased in large quantities ($1 per 650 megabyte disk). This explains why so
much software is sold on CD-ROM today. With desktop CD-ROM recorders,
individuals are able to publish their own CD-ROMs.
With existing methods fast approaching their limits, it is no wonder that a
number of new storage technologies are developing. Currently, researches are looking
at protien-based memory to compete with the speed of electronic memory, the
reliability of magnetic hard-disks, and the capacities of optical/magnetic storage. We
contend that three-dimensional optical memory devices made from bacteriorhodopsin
utilizing the two photon read and write-method is such a technology with which the
future of memory lies.
In a prototype memory system, bacteriorhodopsin stores data in a 3-D matrix.
The matrix can be build by placing the protein into a cuvette (a transparent vessel)
Department of Computer Engineering
2
Protein Based Optical Memory
filled with a polyacrylamide gel. The protein, which is in the bR state, gets fixed in by
the polymerization of the gel. A battery of Krypton lasers and a charge-injection
device (CID) array surround the cuvette and are used to write and read data.
While a molecule changes states within microseconds, the combined steps to
read or write operation take about 10 milliseconds. However like the holographic
storage, this device obtains data pages in parallel, so a 10 Mbps is possible. This
speed is similar to that of slow semiconductor memory.
Department of Computer Engineering
3
Protein Based Optical Memory
2. Memory Research and Development
Semiconductor memories were first developed in 1958 by Jack St. Clair Kilby
was revolutionary for that era but this technology is already showing its age. As the
millennium nears, research into memory technologies is expanding into new
previously unexplored areas for digital storage solutions. These new fields promise to
fulfill the data processing and computational needs of the 21st century. The primary
forms of memory which are currently being explored are optical memory and
molecular memory. One of the reasons why the need for new technologies has arisen
is that the design and construction of smaller and smaller chips is becoming
increasingly difficult. Manufacturers are working with dies in the .18 - .25 micron
range. This will decrease even more but there is a finite limit to how far you can
reduce the die sizes. The restrictions are twofold. One restriction is simply economic.
The cost of producing smaller chips is skyrocketing. More importantly though the
laws of physics will eventually halt this progression of decreasing dies. Moore's law
states that the number of transistors on a chip will double approximately even 18
months and this has held true ever since he made his prediction in the 1960s.
Semiconductor chips are manufactured using a process known as
photolithography where the desired circuit features are mapped onto the silicon via a
mask and a light source. The problem arises though that your light source must be at
least as small as the features you're trying to fashion. This becomes increasingly
difficult as the wavelengths of the spectrum are fixed and will not change. Krypton-
Fluoride ultraviolet laser light is currently being used as the light source for .25
micron mask operations and although the masks can still be smaller, the task becomes
increasingly complex. One developmental system which seeks to overcome these
limitations is optical computing.
Optical computing relies on photons rather than electrons for data transfer.
Electrons although fast have mass and are limited in velocity. Photons on the other
Department of Computer Engineering
4
Protein Based Optical Memory
hand are based on light waves are as such have no mass are travel at the speed of
light. The process of using light to store data is known as holography. Holographic
data storage reads and writes entire blocks in a single operation making it extremely
fast as a storage medium. The parallel nature of the data access means that speeds of
up to 1 Gbps can be achieved and storage densities of 10 GB per cubic centimetre are
capable. Polymer memory cubes exist which allow data to be stored and accessed in
three dimensions making it very fast for optical storage. Another advantage is that the
photons in the optical computer are not subject to electrical or magnetic interference
as are their electronic counterparts. Building a system around photonics isn't as easy
as it sounds though and many years of research and development will be needed
before a successful system can be built. Several groups are working on such a system
though. Researchers from TRW Space Technology Group, the University of
California-Berkley, the National Institute of Standards and Technology, Hewlett-
Package Research Division and Stanford University are all working together in order
to develop a digital computer system based on photonics. One of the difficulties
which arise in building such a machine is that it is much more difficult to construct
hardware which can control the photons. A second alternative to traditional storage
mediums is molecular memory. At first this approach might seem somewhat odd and
possibly insane. However some of the greatest scientific minds in history were
considered insane at the time.
Professor Robert Birge has developed a system to represent binary data using a
protein known as bacteriorhodopsin. One might question why proteins would be used
to store data. Size in general allows proteins to be a good candidate for data storage
and the bacteriorhodopsin was chosen because its sensitivity to light allows it to
change structurally and would be a good representation of a logic gate, the primary
building block of our memory cell. A series of lasers is then used to excite the protein
molecules and read or set their states. Currently speeds of 10 Mbps can be achieved
however Professor Birge is convinced that 80 Mbps can be reached. So currently
molecular memory isn't very fast in comparison to semiconductor memories but its
advantages lie is the cost of developments, storage density, and its non-volatility.
Department of Computer Engineering
5
Protein Based Optical Memory
2.1 Semiconductor Memory Developments
The demands made upon computers and computing devices are increasing
each year. Processor speeds are increasing at an extremely fast clip. However, the
RAM used in most computers is the same type of memory used several years ago. The
limits of making RAM denser are being reached. Surprisingly, these limits may be
economical rather than physical. A decrease by a factor of two in size will increase
the cost of manufacturing of semiconductor pieces by a factor of 5.
Currently, RAM is available in modules called SIMMs or DIMMS. These
modules can be bought in various capacities from a few hundred kilobytes of RAM to
about 64 megabytes. Anything more is both expensive and rare. These modules are
generally 70ns; however 60ns and 100ns modules are available. The lower the
nanosecond rating, the more the module will cost. Currently, a 64MB DIMM costs
over $400. All Dimms are 12cm by 3cm by 1cm or about 36 cubic centimeters.
Whereas a 5 cubic centimeter block of bacteriorhodopsin studded polymer could
theoretically store 512 gigabytes of information. When this comparision is made, the
advantage becomes quite clear. Also, these bacteriorhodopsin modules could also
theoretically run 1000 times faster.
In response to the demand for faster, more compact, and more affordable
memory storage devices, several viable alternatives have appeared in recent years.
Among the most promising approaches include memory storage using holography,
polymer-based memory, and our focus, protein-based memory.
2.2 3-Dimensional Optical Memories
Three-dimensional optical memory storage offers significant promise for the
development of a new generation of ultra-high density RAMs (Birge, Computer, 63).
One of the keys to this process lies in the ability of the protein to occupy different
three-dimensional shapes and form cubic matrices in a polymer gel, allowing for truly
three-dimensional memory storage. The other major component in the process lies in
the use of a two-photon laser process to read and write data. As discussed earlier,